As ligações entre a termodinâmica e a mecânica quântica mostram-se interessantes tópicos de pesquisa desde os anos 50 e tem atraído cada vez mais atenção nos últimos anos, tanto por suas possíveis aplicações tecnológicas, quanto pelo aspecto teórico - como, por exemplo, as relações de sistemas quânticos com a segunda lei da termodinâmica. Para sistemas quânticos mesoscópicos, restritos apenas a um número relativamente pequeno de estados energéticos, torna-se necessária uma generalização da termodinâmica usual. Neste trabalho mostramos como construir uma máquina de Stirling no contexto de íons aprisionados. Para isso, faz-se necessária a engenharia de frequências dependentes do tempo do modo vibracional do íon, além da engenharia de reservatórios térmicos com temperaturas controladas. Após a construção da máquina de Stirling e do cálculo do trabalho e da eficiência associados apresentamos um protocolo para a medida da função de distribuição do trabalho que recorre às medidas dos níveis de energia eletrônicos do íon para, a partir dessas, extrair-se informação sobre o seu estado vibracional. / The connections between quantum mechanics and thermodynamics have been an interesting research topic since the 1950´s and began attracting more and more attention recently, not only for the technological applications, but also from a theoretical point of view - as, for instance, when dealing with the relations between quantum systems and the second law of thermodynamics. For mesoscopic (or even macroscopic) quantum systems, restricted to relatively few energy states, a generalization of the usual thermodynamics becomes necessary. In the present work we show how to engeneer a Stirling engine in an ionic trap. To achieve this we have to engeneer an ionic vibrational mode with a time dependent frequency, and simutaneously engeneer a thermal reservoir with controled temperatures. After the construction of the Stirling machine and the calculation of the associated work and efficiency, we show a protocol that allows the measurement of the work distribution function which call on the measurement of the electronic energy levels of the ion and, from them, extract information about the vibrational state of the trap.

As ligações entre a termodinâmica e a mecânica quântica mostram-se interessantes tópicos de pesquisa desde os anos 50 e tem atraído cada vez mais atenção nos últimos anos, tanto por suas possíveis aplicações tecnológicas, quanto pelo aspecto teórico - como, por exemplo, as relações de sistemas quânticos com a segunda lei da termodinâmica. Para sistemas quânticos mesoscópicos, restritos apenas a um número relativamente pequeno de estados energéticos, torna-se necessária uma generalização da termodinâmica usual. Neste trabalho mostramos como construir uma máquina de Stirling no contexto de íons aprisionados. Para isso, faz-se necessária a engenharia de frequências dependentes do tempo do modo vibracional do íon, além da engenharia de reservatórios térmicos com temperaturas controladas. Após a construção da máquina de Stirling e do cálculo do trabalho e da eficiência associados apresentamos um protocolo para a medida da função de distribuição do trabalho que recorre às medidas dos níveis de energia eletrônicos do íon para, a partir dessas, extrair-se informação sobre o seu estado vibracional. / The connections between quantum mechanics and thermodynamics have been an interesting research topic since the 1950´s and began attracting more and more attention recently, not only for the technological applications, but also from a theoretical point of view - as, for instance, when dealing with the relations between quantum systems and the second law of thermodynamics. For mesoscopic (or even macroscopic) quantum systems, restricted to relatively few energy states, a generalization of the usual thermodynamics becomes necessary. In the present work we show how to engeneer a Stirling engine in an ionic trap. To achieve this we have to engeneer an ionic vibrational mode with a time dependent frequency, and simutaneously engeneer a thermal reservoir with controled temperatures. After the construction of the Stirling machine and the calculation of the associated work and efficiency, we show a protocol that allows the measurement of the work distribution function which call on the measurement of the electronic energy levels of the ion and, from them, extract information about the vibrational state of the trap.

Landauer's principle states that it costs at least k_BT ln 2 of work to reset one bit in the presence of a heat bath at temperature T. The bound of k_BT ln 2 is achieved in the unphysical infinite-time limit. Here we consider two different finite-time protocols - one with discretised time and the second in the continuous limit. We prove analytically that the discrete time protocol enables one to reset a bit with a work cost close to k_BT ln 2 in a finite time. We construct an explicit protocol that achieves this, which involves thermalising and changing the system's Hamiltonian so as to avoid quantum coherences. Using concepts and techniques pertaining to single-shot statistical mechanics, we furthermore prove that the heat dissipated is exponentially close to the minimal amount possible not just on average, but guaranteed with high confidence in every run. Moreover we exploit the protocol to design a quantum heat engine that works near the Carnot efficiency in finite time. We further contrast this to a continuous time version of the protocol which is substantially less energy sufficient. We also consider the fluctuations in the work cost, and calculate how their magnitude is suppressed by a factor depending on the length of the protocol. We demonstrate with an experiment how molecules are a natural test-bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. By considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states, we demonstrate that the quantum Jarzynski equality is satisfied in this set-up. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.

[pt] A Igualdade de Jarzynski (IJ) é um tipo especial de Teorema de Flutuação, de trabalho, que caracteriza sistemas termodinâmicos microscópicos fora do equilíbrio. A IJ pode ser usada como uma calibração de experimentos e simulações, o que nos permite estudar comportamentos não triviais da dinâmica desses sistemas. Um desses comportamentos é a troca de entropia e informação que o sistema realiza junto a um banho térmico de contato. Neste ensejo, modelamos via uma dinâmica não-Markoviana, i.e., uma dinâmica com memória, que leva a fluxos reversos de informação do reservatório para o sistema. / [en] The Jarzynski Equality (JE) is a special kind of Fluctuation Theorem, of work, which characterizes non-equilibrium small thermodynamics systems. The JE can be used as gauge of experiments and simulations allowing us to study the non-trivial behaviours of these systems dynamics. One of these behaviours is the entropy and information flow the system makes in contact with a thermal bath. In this framework, we modelled through a non-Markovian dynamic, i.e., with a memory effect, leading to reverse flows of information from the reservoir to the system.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Nonequilibrium work theorems, such as the Jarzynski equality and the Crooks fluctuation theorem, allow one to use nonequilibrium measurements to determine equilibrium free energies. For example, it has been demonstrated that the Crooks fluctuation theorem can be used to determine RNA folding energies. We used single-molecule manipulation with an atomic force microscope to measure the work done on poly(dA) as it was stretched and relaxed. This single-stranded nucleic acid exhibits unique base-stacking transitions in its force-extension curve due to the strong interactions among A bases, as well as multiple pathways. Here we showed that free energy curves can be determined by using the Crooks fluctuation theorem. The nonequilibrium work theorem can be used to determine free energy curves even when there are multiple pathways.

Submitted by Luiz Felipe Barbosa (luiz.fbabreu2@ufpe.br) on 2015-04-17T12:53:01Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DISSERTAÇÃO Annielle Silva.pdf: 4594171 bytes, checksum: 51d05b433109819b0c9846edafc2af58 (MD5) / Made available in DSpace on 2015-04-17T12:53:01Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DISSERTAÇÃO Annielle Silva.pdf: 4594171 bytes, checksum: 51d05b433109819b0c9846edafc2af58 (MD5) Previous issue date: 2013-02-28 / CAPES CNPq INAMI / O nanoporo formado pela incorporação da α-hemolisina em bicamadas lipídicas planas é considerado modelo de nanoporo proteico para elucidação do mecanismo de transporte de moléculas e no desenvolvimento de dispositivos analíticos - biossensores, espectrômetros de massa e sequenciadores moleculares. O conhecimento da interação de nucleotídeos com o nanoporo da α-hemolisina é de especial interesse, pois, alguns estudos sugerem varias metodologias para a utilização deste nanoporo como sequenciador de DNA em tempo real. Apesar de todos os avanços, a principal dificuldade operacional para obtenção de um sequenciador baseado na tecnologia “nanopore sensing”, é a rapidez na translocação do DNA através do nanoporo; dificultando a discriminação adequada das bases. Neste contexto é imprescindível fazer adaptações moleculares no nanoporo visando o aumento do tempo de permanência do DNA e da energia de interação deste com o nanoporo. As principais estratégias disponíveis para produção de nanoporos adaptados são: mutações sítio dirigidas e funcionalização química. Ambas são de elevado custo e tempo de experimentação. Neste trabalho utilizamos técnicas de simulação computacional para obtenção, a nível atomístico, a interação do DNA com o nanoporo da α-hemolisina na sua forma nativa e adaptada em posições estratégicas previamente selecionadas por modelagem molecular. As técnicas utilizadas baseiam-se na dinâmica molecular fora do equilíbrio e na Relação de Jarzynski, na qual a média do trabalho realizado ao deslocar o DNA ao longo do nanoporo proteico é estatisticamente relacionada à energia livre do processo. As informações sobre as interações do DNA-nanoporo obtidas podem predizer, teoricamente, os nanoporos mais promissores para serem testados experimentalmente. Realizou-se a seleção das mutantes que foram usadas e foram obtidos dados importantes sobre a parametrização das dinâmicas usando a relação de Jarzynski, como velocidade e constante de força que devem ser aplicadas ao sistema. Além disso, foram obtidas informações sobre a trajetória e contato do DNA com o interior do poro mutado e na forma selvagem, o que mostra a efetividade do sistema.

Indiana University-Purdue University Indianapolis (IUPUI) / Open quantum systems have become a rapidly developing sector for research. Such systems present novel physical phenomena, such as topological chirality, enhanced sensitivity, and unidirectional invisibility resulting from both their non-equilibrium dynamics and the presence of exceptional points. We begin by introducing the core features of open systems governed by non-Hermitian Hamiltonians, providing the PT -dimer as an illustrative example. Proceeding, we introduce the Lindblad master equation which provides a working description of decoherence in quantum systems, and investigate its properties through the Decohering Dimer and periodic potentials. We then detail our preferred experimental apparatus governed by the Lindbladian. Finally, we introduce the Liouvillian, its relation to non-Hermitian Hamiltonians and Lindbladians, and through it investigate multiple properties of open quantum systems.